Previous mail filters no longer working with new

I work at an university office, in charge of emails for online forms, a specific email set up for forms only. As we have several different forms, I have a large set of mail filters which were all working just fine. We had a new form go live so I set up another large set of filters (because of different majors, etc., I had to set up one for each). They seemed to work fine during my testing but all the sudden, my older filters have stopped working or are picking up parts of new filters.

My new filters are for Graduation Applications and are forwarded to the auditors' email and filed in a folder called Grad App. My old filter, for example Prerequisite Waiver, instead of being filed in its folder, Prereq Waiver, as the filter is set, it is now going to my Grad App folder and is forwarded to the auditor.

My filter for the Prerequisite is set as:
If any of the following conditions are met:Subject contains PrerequisiteFile into folder Pre-req
*Do not process additional filters

The Graduation Application filter is:
If any of the following conditions are met:Subject contains Audit1, 201210, UG, majorFile into folder Grad AppForward to Address auditor
*Do not process additional filters

Now, the subjects for neither Prerequisites nor Graduation Applications contain the words the other has and yet they are all routing to the Grad App folder even though the filter has it set different. This isn't just happening with Prerequisites though. It's also causing problems with other emails, those for Course Substitutions, Waivers, Withdrawals, all of which have unique subject headers and/or body. I can't figure out why they all are routing to the Grad App folder.

Another issue is a form for Exemptions, which has no filter, is also going to Grad App folder, rather than the Inbox. There are certain emails that do not get filters because they must be dealt with on an email-by-email basis so they should simply go to the Inbox, not be routed to a folder or specific email. I have tried several different ways to fix this but unfortunately I can't seem to find a way.